Polymethine compounds and their use as fluorescent labels

1. A compound of the formula (I), or a mesomeric form thereof:

wherein mCat+ or mAn− is an organic or inorganic positively/negatively charged counterion;

m is 0, 1, 2 or 3;

p is 1 or 2;

q is 1, 2, 3 4 or 5;

alk is a chain of 1-5 carbon atoms optionally containing one or more double or triple bonds;

Y is CH2;

Z is OH;

n is 0, 1, 2 or 3;

X is OH or O − , or an amide or ester conjugate thereof;

each of Ra 1 and Ra 2 is independently H, SO 3 − , sulfonamide, halogen, or a further ring fused to an adjacent carbon atom; and

each of Rc 1 and Rc 2 is independently alkyl or substituted alkyl, wherein at least one of Ra 1 or Ra 2 is SO 3 − , or Ra 1 or Ra 2 is a further ring fused to an adjacent carbon atom, the further ring having an SO 3 − , or Rc 1 or Rc 2 is an alkyl sulfonic acid group.

2. The compound of claim 1 , wherein (alk) is (CH 2 ) 1-5 .

3. The compound of claim 1 , wherein each of Ra 1 and Ra 2 is H or SO 3 − .

4. The compound of claim 1 , wherein Ra 1 or Ra 2 is a further ring fused to an adjacent carbon atom.

5. The compound of claim 4 , wherein either indole moiety of formula (I) is part of a structure:

wherein Rd is H, alkyl, substituted alkyl, aryl, substituted aryl, halogen, carboxy, sulfonamide, or sulfonic acid; and wherein Rc 1 is alkyl or substituted alkyl.

6. The compound of claim 1 , wherein each of Rc 1 and Rc 2 is independently methyl, ethyl, propyl or —(CH 2 ) t SO 3 − , where t is 1-6.

7. The compound of claim 6 , wherein one of Rc 1 or Rc 2 is methyl and the other one of Rc 1 or Rc 2 is —(CH 2 ) 4 —SO 3 − .

8. The compound of claim 1 , wherein X is OH and q is 5.

9. The compound of claim 1 , selected from the group consisting of:

and salts and mesomeric forms thereof.

10. A nucleotide labelled with a compound according to claim 1 .

11. The nucleotide of claim 10 , wherein the compound is attached to the nucleotide or oligonucleotide via an amide linkage formed from the C(═O)—X moiety.

12. The nucleotide of claim 11 , wherein the compound is attached to the C5 position of a pyrimidine base or the C7 position of a 7-deaza purine base of the nucleotide or oligonucleotide through a linker moiety.

13. The nucleotide of claim 12 , further comprising a 3′ OH blocking group covalently attached to the ribose or deoxyribose sugar of the nucleotide or oligonucleotide.

14. The nucleotide of claim 13 , wherein the nucleotide is a nucleoside triphosphate, and wherein the 3′ OH blocking group is covalently attached to the 2-deoxyribose sugar of the nucleotide.

15. An oligonucleotide comprising a labeled nucleotide residue of claim 14 , wherein the nucleotide is incorporated into the oligonucleotide through formation of a phosphodiester linkage with the 5′ phosphate group of the nucleotide.

16. A kit comprising two or more different types of nucleotides, wherein at least one type of nucleotide is a labelled nucleotide according to claim 10 .

17. The kit according to claim 16 , comprising four different types of nucleotides, wherein a first type of nucleotide is a labelled nucleotide according to claim 10 , and the second, third, and fourth type of nucleotides are each labelled with a different compound, wherein each compound has a distinct absorbance maximum and each of the compounds is distinguishable from the other three compounds.

18. The kit according to claim 16 , comprising four different types of nucleotides, wherein a first type of nucleotide is a labelled nucleotide according to claim 10 , a second type of nucleotide is a labelled with a spectrally distinct compound, a third type of nucleotide carries a mixture of two labels, and a fourth type of nucleotide is unlabelled (dark).

19. The kit of claim 16 , wherein the different types of nucleotides are excited using a single laser or two lasers with different wavelengths.

20. The kit of claim 19 , wherein at least one laser has the wavelength from about 488 nm to about 550 nm, or about 532 nm.